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- EMDB-1121: Mapping the structure and function of the E1 and E2 glycoproteins... -

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Basic information

Entry
Database: EMDB / ID: 1121
TitleMapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
SampleSindbis TE12 E2-N318Q
SourceSindbis virus / virus / Sindbis strain TE12 / シンドビスウイルス
Map datacenter of virus is where z=0
Methodsingle particle (icosahedral) reconstruction, at 9 A resolution
AuthorsMukhopadhyay S / Zhang W / Gabler S / Chipman PR / Strauss EG / Strauss JH / Baker TS / Kuhn RJ / Rossmann MG
CitationStructure, 2006, 14, 63-73

Structure, 2006, 14, 63-73 StrPapers
Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
Suchetana Mukhopadhyay / Wei Zhang / Stefan Gabler / Paul R Chipman / Ellen G Strauss / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann

DateDeposition: Apr 8, 2005 / Header (metadata) release: Apr 8, 2005 / Map release: Jan 16, 2006 / Last update: Apr 8, 2005

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 75
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 75
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-1z8y
  • Surface level: 100
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-2xfb
  • Surface level: 100
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3muw
  • Surface level: 100
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1121.map.gz (map file in CCP4 format, 335025 KB)
Projections & slices
Size
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Others
AxesZ (Sec.)X (Row.)Y (Col.)
441 pix
1.78 A/pix
= 787.18 A
441 pix
1.78 A/pix
= 787.18 A
441 pix
1.78 A/pix
= 787.18 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.78499 A
Density
Contour Level:138, 75 (movie #1):
Minimum - Maximum-297.65 - 402.47
Average (Standard dev.)7.03224 (65.0912)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions441441441
Origin-220-220-220
Limit220220220
Spacing441441441
CellA=B=C: 787.18 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.78498866213151.78498866213151.7849886621315
M x/y/z441441441
origin x/y/z0.0000.0000.000
length x/y/z787.180787.180787.180
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ441441441
MAP C/R/S213
start NC/NR/NS-220-220-220
NC/NR/NS441441441
D min/max/mean-297.650402.4707.032

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Supplemental data

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Sample components

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Entire Sindbis TE12 E2-N318Q

EntireName: Sindbis TE12 E2-N318Q
Details: Sample is a single deglycosylated virus. For mutagenesis and purification, please see Pletnev et al. (2001) Cell. Virus contains 3 proteins (E1, E2, capsid), a lipid bilyer, and a positive-strand RNA genome.
Number of components: 1

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Component #1: virus, Sindbis virus

VirusName: Sindbis virus / a.k.a: Sindbis strain TE12 / Class: VIRION / Details: deglycosylated virus / Empty: No / Enveloped: Yes / Isolate: STRAIN
MassExperimental: 52 MDa
SpeciesSpecies: Sindbis virus / virus / Sindbis strain TE12 / シンドビスウイルス
Source (natural)Host Species: Homo sapiens / human / Host category: INVERTEBRATES
Shell #1Name of element: glycoprotein / Diameter: 710 A / T number(triangulation number): 4
Shell #2Name of element: lipid bilayer / Diameter: 480 A / T number(triangulation number): 4
Shell #3Name of element: capsid / Diameter: 410 A / T number(triangulation number): 4

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 6 mg/ml / Buffer solution: 20 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA / pH: 7.4
Support filmholey carbon 400 mesh copper grid
Stainingno staining
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: standard methods / Time resolved state: Vitrified immediately after blotting.
Details: Vitrification instrument: Purdue manufactured, gravity driven device. Vitrification carried out in hood.

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200T / Date: Jun 21, 2000 / Details: Low dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal), 39220 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1100 - 2580 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: K ( 87 - 100 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 27 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / OD range: 1 / Details: optical density range is 0.33-1.35

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 7085 / Number of class averages: 3
Details: The particles were selected interactively at the computer terminal.
Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: model-based common lines / Software: Purdue Suite / CTF correction: CTF correction of each particle. / Resolution: 9 A / Resolution method: FSC 0.5
Euler angles: Euler angles (theta, phi, omega) are defined as three successive rotations in a right hand coordinate system. First, the viewer is rotated counterclockwise around the z-axis (angle 'phi') and then rotated counterclockwise around the new y-axis (angle 'theta') and rotate clockwise around the new z-axis (angle 'omega').
Details: resolution determined by splitting data set into two groups.

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Atomic model buiding

Modeling #1Software: EMFIT / Refinement protocol: rigid body / Target criteria: sumf / Refinement space: REAL
Details: Protocol: Rigid body. each protein in the asymmetric unit was fitting individually.
Input PDB model: 1I9W
Modeling #2Software: EMFIT / Refinement protocol: rigid body / Target criteria: sumf / Refinement space: REAL
Details: Protocol: Rigid body. each protein in the asymmetric unit was fitting individually.
Input PDB model: 1XYK
Output model

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